Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Abstract

BackgroundThe process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly.ResultsIn Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies.ConclusionsMany current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.

A reference genome of the Chinese hamster based on a hybrid assembly strategy

“…Second, further improvements of the assembly attributes were obtained by merging the single-platform assemblies. Previously, assembly merging with Metassembler was found to modestly improve the starting assemblies [Bradnam et al, 2013]. Here, we obtained large gains in the N50, with the PICR metassembly being ~4x more contiguous than the starting assemblies.…”

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

“…In total, 237 of 248 CEGs were completely present, and 7 CEGs were partially present, indicating that fewer than 2% of the CEGs could not be detected, which compared very favorably with other assemblies 31 .…”

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

“…New reference-quality sequence sources are needed, because generation of finished sequence from clone libraries is in significant decline due to cost and some remaining assembly gaps occur in regions recalcitrant to cloning. A growing collection of human genomes in INSDC databases, a prerequisite for any sequence that will contribute to the reference assembly, that were sequenced and assembled with new technologies are candidates for use in assembly improvement (Earl et al 2011;Vezzi et al 2012;Bradnam et al 2013;English et al 2015;Pendleton et al 2015;Seo et al 2016;Shi et al 2016;Zook et al 2016). However, WGS assembly sequences have historically not been considered reference quality, raising concerns about their use in reference genome assembly curation.…”